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Cobalt in PDB 4lpn: Frog M-Ferritin with Cobalt, D127E Mutant

Enzymatic activity of Frog M-Ferritin with Cobalt, D127E Mutant

All present enzymatic activity of Frog M-Ferritin with Cobalt, D127E Mutant:
1.16.3.1;

Protein crystallography data

The structure of Frog M-Ferritin with Cobalt, D127E Mutant, PDB code: 4lpn was solved by R.Torres, R.Behera, C.W.Goulding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.00 / 1.66
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.003, 184.003, 184.003, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 17.7

Other elements in 4lpn:

The structure of Frog M-Ferritin with Cobalt, D127E Mutant also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 9 atoms

Cobalt Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Cobalt atom in the Frog M-Ferritin with Cobalt, D127E Mutant (pdb code 4lpn). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 11 binding sites of Cobalt where determined in the Frog M-Ferritin with Cobalt, D127E Mutant, PDB code: 4lpn:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 11 in 4lpn

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Cobalt binding site 1 out of 11 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co201

b:24.7
occ:0.70
OE1 A:GLU23 2.0 22.2 1.0
OE1 A:GLU58 2.0 30.7 1.0
O A:HOH464 2.1 28.4 1.0
O A:HOH415 2.2 26.6 1.0
ND1 A:HIS61 2.3 25.5 1.0
CD A:GLU23 2.8 26.0 1.0
CD A:GLU58 3.0 30.7 1.0
OE2 A:GLU23 3.0 23.5 1.0
CE1 A:HIS61 3.2 32.0 1.0
HG11 A:VAL106 3.2 18.4 1.0
HE1 A:HIS61 3.3 38.4 1.0
CG A:HIS61 3.3 20.2 1.0
HB2 A:HIS61 3.4 19.3 1.0
HA A:GLU58 3.4 15.3 1.0
OE2 A:GLU58 3.5 41.3 1.0
HB3 A:HIS61 3.6 19.3 1.0
CB A:HIS61 3.7 16.1 1.0
OE1 A:GLN137 3.8 32.8 0.6
CO A:CO202 3.9 39.0 0.2
CG1 A:VAL106 4.1 15.3 1.0
HB3 A:GLU58 4.2 19.3 1.0
OE1 A:GLN137 4.2 21.8 0.4
CG A:GLU23 4.2 16.0 1.0
CG A:GLU58 4.3 17.1 1.0
HB3 A:GLU23 4.3 16.1 1.0
HA A:GLU23 4.3 15.1 1.0
HG13 A:VAL106 4.3 18.4 1.0
CA A:GLU58 4.3 12.7 1.0
NE2 A:HIS61 4.3 27.2 1.0
O A:HOH392 4.4 20.9 1.0
CD2 A:HIS61 4.4 25.6 1.0
O A:HOH481 4.4 46.4 1.0
HG12 A:VAL106 4.5 18.4 1.0
CB A:GLU58 4.5 16.1 1.0
HG21 A:VAL106 4.5 17.2 1.0
HD2 A:TYR133 4.6 18.2 1.0
CD A:GLN137 4.7 22.1 0.6
CB A:GLU23 4.7 13.4 1.0
HG3 A:GLU23 4.7 19.2 1.0
HE2 A:TYR133 4.8 17.3 1.0
HG2 A:GLU23 4.8 19.2 1.0
HE22 A:GLN137 4.8 30.6 0.4
HE22 A:GLN137 4.8 26.3 0.6
HG3 A:GLU58 4.8 20.5 1.0
O A:GLU58 4.8 15.8 1.0
HG2 A:GLU58 4.9 20.5 1.0
HG2 A:GLU57 4.9 36.1 0.6
HB3 A:ALA26 5.0 14.6 1.0

Cobalt binding site 2 out of 11 in 4lpn

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Cobalt binding site 2 out of 11 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co202

b:39.0
occ:0.25
OE2 A:GLU58 2.0 41.3 1.0
O A:HOH464 2.1 28.4 1.0
OE1 A:GLU103 2.1 28.8 1.0
OE2 A:GLU103 2.1 39.9 1.0
O A:HOH481 2.1 46.4 1.0
CD A:GLU103 2.3 30.5 1.0
CO A:CO203 2.7 50.6 0.2
HE22 A:GLN137 2.8 30.6 0.4
HE22 A:GLN137 2.8 26.3 0.6
CD A:GLU58 3.0 30.7 1.0
OE1 A:GLU58 3.4 30.7 1.0
OE1 A:GLN137 3.5 32.8 0.6
NE2 A:GLN137 3.5 25.5 0.4
NE2 A:GLN137 3.6 21.9 0.6
HE2 A:TYR30 3.6 20.2 0.5
HE2 A:TYR30 3.7 19.9 0.5
OE1 A:GLN137 3.7 21.8 0.4
CG A:GLU103 3.7 17.0 1.0
HA A:GLU103 3.8 17.1 1.0
HH A:TYR30 3.8 21.0 0.5
CO A:CO201 3.9 24.7 0.7
CD A:GLN137 4.0 22.1 0.6
HG2 A:GLU103 4.0 20.4 1.0
CD A:GLN137 4.0 21.1 0.4
HG11 A:VAL106 4.1 18.4 1.0
HE21 A:GLN137 4.2 30.6 0.4
HG21 A:VAL106 4.2 17.2 1.0
CG A:GLU58 4.3 17.1 1.0
HB3 A:GLU103 4.3 20.4 1.0
HG3 A:GLU103 4.3 20.4 1.0
HE21 A:GLN137 4.3 26.3 0.6
HE1 A:HIS61 4.4 38.4 1.0
HB A:VAL106 4.4 17.2 1.0
OD2 A:ASP140 4.4 41.6 1.0
CB A:GLU103 4.4 17.0 1.0
OH A:TYR30 4.4 28.6 0.5
HG3 A:GLU58 4.5 20.5 1.0
HG2 A:GLU58 4.5 20.5 1.0
CE2 A:TYR30 4.5 16.6 0.5
CE2 A:TYR30 4.5 16.8 0.5
CA A:GLU103 4.6 14.3 1.0
OH A:TYR30 4.6 17.5 0.5
HB1 A:ALA26 4.8 14.6 1.0
HB3 A:ASP140 4.8 23.6 1.0
O A:HOH415 4.8 26.6 1.0
HB2 A:ASP140 4.8 23.6 1.0
CG1 A:VAL106 4.9 15.3 1.0
OE1 A:GLU57 4.9 29.9 0.6
CB A:VAL106 4.9 14.3 1.0
CZ A:TYR30 5.0 16.5 0.5
CG2 A:VAL106 5.0 14.3 1.0

Cobalt binding site 3 out of 11 in 4lpn

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Cobalt binding site 3 out of 11 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co203

b:50.6
occ:0.25
OE2 A:GLU103 2.2 39.9 1.0
OE2 A:GLU58 2.2 41.3 1.0
O A:HOH481 2.3 46.4 1.0
ND1 A:HIS54 2.5 29.3 1.0
CO A:CO202 2.7 39.0 0.2
HE2 A:TYR30 2.8 20.2 0.5
HH A:TYR30 3.1 21.0 0.5
HE1 A:HIS54 3.2 57.2 1.0
CE1 A:HIS54 3.2 47.7 1.0
HE2 A:TYR30 3.2 19.9 0.5
CD A:GLU103 3.2 30.5 1.0
CD A:GLU58 3.4 30.7 1.0
CE2 A:TYR30 3.4 16.8 0.5
HG2 A:GLU58 3.5 20.5 1.0
HB3 A:HIS54 3.5 20.6 1.0
CG A:HIS54 3.6 25.9 1.0
OE1 A:GLU103 3.7 28.8 1.0
OD2 A:ASP140 3.7 41.6 1.0
OH A:TYR30 3.7 17.5 0.5
CE2 A:TYR30 3.8 16.6 0.5
OE1 A:GLU57 3.8 29.9 0.6
CZ A:TYR30 3.9 15.4 0.5
CG A:GLU58 3.9 17.1 1.0
CB A:HIS54 4.1 17.1 1.0
CD A:GLU57 4.1 35.9 0.6
HG3 A:GLU58 4.2 20.5 1.0
O A:HOH464 4.2 28.4 1.0
HA A:HIS54 4.3 14.4 1.0
CD2 A:TYR30 4.3 15.1 0.5
HB3 A:ASP140 4.3 23.6 1.0
OH A:TYR30 4.4 28.6 0.5
CZ A:TYR30 4.4 16.5 0.5
O A:HIS54 4.4 14.7 1.0
OE2 A:GLU57 4.4 40.2 0.6
HD2 A:TYR30 4.4 18.1 0.5
HB3 A:GLU57 4.4 28.3 0.6
OE1 A:GLU58 4.4 30.7 1.0
NE2 A:HIS54 4.4 38.8 1.0
CG A:ASP140 4.5 27.3 1.0
CD2 A:TYR30 4.5 14.8 0.5
HD2 A:TYR30 4.5 17.8 0.5
HB2 A:GLU57 4.5 28.4 0.4
CG A:GLU103 4.5 17.0 1.0
HG2 A:GLU57 4.5 36.1 0.6
CA A:HIS54 4.6 12.0 1.0
CD2 A:HIS54 4.7 34.6 1.0
HG3 A:GLU103 4.7 20.4 1.0
OE1 A:GLU57 4.7 38.0 0.4
HG2 A:GLU103 4.7 20.4 1.0
HE1 A:HIS61 4.7 38.4 1.0
CO A:CO204 4.8 43.8 0.5
CG A:GLU57 4.8 30.1 0.6
CB A:ASP140 4.8 19.6 1.0
C A:HIS54 4.9 13.3 1.0
HB2 A:HIS54 4.9 20.6 1.0
HB2 A:ASP140 5.0 23.6 1.0

Cobalt binding site 4 out of 11 in 4lpn

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Cobalt binding site 4 out of 11 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co204

b:43.8
occ:0.50
OE2 A:GLU136 1.8 25.7 0.4
O A:HOH475 2.1 43.0 1.0
OE1 A:GLU57 2.2 29.9 0.6
OE2 A:GLU57 2.2 40.2 0.6
OD1 A:ASP140 2.2 27.3 1.0
OD2 A:ASP140 2.2 41.6 1.0
CD A:GLU57 2.5 35.9 0.6
CG A:ASP140 2.5 27.3 1.0
CD A:GLU136 2.8 28.5 0.4
HG2 A:GLU136 3.1 28.2 0.6
OE1 A:GLU136 3.2 31.6 0.6
OE1 A:GLU57 3.3 38.0 0.4
OE1 A:GLU136 3.4 33.6 0.4
HE1 A:HIS54 3.4 57.2 1.0
HG3 A:GLU136 3.6 28.2 0.6
CG A:GLU136 3.7 23.5 0.6
CD A:GLU136 3.8 32.3 0.6
CD A:GLU57 3.9 34.1 0.4
CE1 A:HIS54 3.9 47.7 1.0
CG A:GLU57 4.0 30.1 0.6
HG3 A:GLU136 4.0 33.8 0.4
CG A:GLU136 4.0 28.2 0.4
CB A:ASP140 4.1 19.6 1.0
O A:HOH481 4.1 46.4 1.0
OE2 A:GLU57 4.1 39.1 0.4
HG3 A:GLU57 4.2 36.1 0.6
HG2 A:GLU136 4.3 33.8 0.4
HB3 A:ASP140 4.4 23.6 1.0
HG2 A:GLU57 4.5 36.1 0.6
ND1 A:HIS54 4.5 29.3 1.0
HB3 A:GLU57 4.5 28.4 0.4
HB2 A:ASP140 4.5 23.6 1.0
NE2 A:HIS54 4.6 38.8 1.0
O A:GLU136 4.6 18.2 0.4
HA A:ASP140 4.6 18.3 1.0
O A:GLU136 4.7 17.3 0.6
HE1 A:HIS61 4.7 38.4 1.0
HE2 A:HIS54 4.8 46.5 1.0
CO A:CO203 4.8 50.6 0.2
CA A:ASP140 4.9 15.2 1.0
HB2 A:GLU57 4.9 28.3 0.6
CG A:GLU57 5.0 23.5 0.4
HB2 A:GLU57 5.0 28.4 0.4
H A:ASP140 5.0 16.1 1.0
CB A:GLU57 5.0 23.6 0.6
HB3 A:GLU57 5.0 28.3 0.6

Cobalt binding site 5 out of 11 in 4lpn

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Cobalt binding site 5 out of 11 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co205

b:11.7
occ:0.25
NE2 A:HIS169 2.2 10.6 1.0
O A:HOH317 2.2 17.3 0.2
CL A:CL212 2.3 12.6 0.2
CE1 A:HIS169 3.0 11.8 1.0
HE1 A:HIS169 3.1 14.1 1.0
CD2 A:HIS169 3.3 13.1 1.0
HD2 A:HIS169 3.5 15.7 1.0
ND1 A:HIS169 4.2 12.0 1.0
CG A:HIS169 4.4 12.9 1.0
HD1 A:HIS169 4.9 14.4 1.0
HD22 A:LEU165 5.0 19.1 1.0

Cobalt binding site 6 out of 11 in 4lpn

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Cobalt binding site 6 out of 11 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co206

b:13.0
occ:0.33
OE2 A:GLU127 2.0 14.2 1.0
CL A:CL219 2.1 18.8 0.3
CD A:GLU127 2.9 13.0 1.0
OE1 A:GLU127 3.1 14.0 1.0
HB3 A:SER131 3.4 21.0 1.0
CO A:CO207 3.9 18.8 0.3
O A:HOH366 4.2 21.5 1.0
CB A:SER131 4.3 17.5 1.0
CG A:GLU127 4.3 12.5 1.0
HB2 A:SER131 4.3 21.0 1.0
HG3 A:GLU127 4.5 15.0 1.0
HG2 A:GLU127 4.6 15.0 1.0
O A:HOH361 4.9 30.0 1.0
HA A:SER131 5.0 19.7 1.0

Cobalt binding site 7 out of 11 in 4lpn

Go back to Cobalt Binding Sites List in 4lpn
Cobalt binding site 7 out of 11 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co207

b:18.8
occ:0.33
OE1 A:GLU127 2.1 14.0 1.0
OE1 A:GLU130 2.1 18.3 1.0
CD A:GLU127 3.3 13.0 1.0
CD A:GLU130 3.4 18.0 1.0
O A:HOH396 3.8 20.6 1.0
HA A:GLU127 3.9 15.3 1.0
CO A:CO206 3.9 13.0 0.3
OE2 A:GLU127 4.0 14.2 1.0
HB2 A:GLU130 4.0 17.8 1.0
HB2 A:GLU127 4.0 16.8 1.0
OE2 A:GLU130 4.1 19.5 1.0
HB3 A:GLU130 4.1 17.8 1.0
CB A:GLU130 4.4 14.9 1.0
CG A:GLU130 4.5 14.7 1.0
CG A:GLU127 4.5 12.5 1.0
CB A:GLU127 4.5 14.0 1.0
CA A:GLU127 4.6 12.7 1.0
CO A:CO209 4.7 31.4 0.3
HG2 A:GLU130 4.8 17.6 1.0
HG2 A:GLU127 4.9 15.0 1.0

Cobalt binding site 8 out of 11 in 4lpn

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Cobalt binding site 8 out of 11 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co208

b:87.2
occ:0.50
OE1 A:GLU63 2.1 42.5 1.0
OE2 A:GLU60 2.1 62.9 1.0
CD A:GLU63 3.0 53.7 1.0
OE2 A:GLU63 3.1 47.7 1.0
CD A:GLU60 3.2 58.2 1.0
OE1 A:GLU60 3.8 65.0 1.0
HA A:GLU60 4.1 19.2 1.0
HG2 A:GLU60 4.1 31.1 1.0
CG A:GLU60 4.3 25.9 1.0
CG A:GLU63 4.4 28.1 1.0
HB2 A:GLU63 4.5 22.0 1.0
HB3 A:GLU63 4.8 22.0 1.0
CB A:GLU63 4.8 18.4 1.0
HG2 A:GLU63 4.9 33.7 1.0
HE2 A:HIS56 4.9 31.0 0.6
HG3 A:GLU63 4.9 33.7 1.0
CA A:GLU60 4.9 16.0 1.0

Cobalt binding site 9 out of 11 in 4lpn

Go back to Cobalt Binding Sites List in 4lpn
Cobalt binding site 9 out of 11 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co209

b:31.4
occ:0.30
O A:HOH440 2.1 26.3 1.0
O A:HOH396 2.1 20.6 1.0
OE2 A:GLU130 3.8 19.5 1.0
O A:HOH319 4.1 19.6 1.0
O A:HOH405 4.1 26.0 1.0
OE1 A:GLU130 4.4 18.3 1.0
CD A:GLU130 4.5 18.0 1.0
CO A:CO207 4.7 18.8 0.3
HB3 A:CYS126 4.7 13.8 1.0
HE2 A:HIS114 4.8 19.2 1.0
HE1 A:HIS114 4.8 18.8 1.0

Cobalt binding site 10 out of 11 in 4lpn

Go back to Cobalt Binding Sites List in 4lpn
Cobalt binding site 10 out of 11 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co210

b:33.9
occ:0.60
O A:HOH424 2.1 35.9 1.0
O A:HOH366 2.1 21.5 1.0
O A:HOH361 2.1 30.0 1.0
O A:HOH445 2.2 32.5 1.0
O A:HOH394 2.2 28.0 1.0
O A:HOH434 3.9 30.4 1.0
OG A:SER131 4.2 16.3 1.0
HB2 A:SER131 4.2 21.0 1.0
CL A:CL219 4.7 18.8 0.3
CB A:SER131 4.7 17.5 1.0
OE2 A:GLU132 4.8 34.1 1.0
HG3 A:GLU127 4.8 15.0 1.0
OE2 A:GLU127 4.8 14.2 1.0
HG A:SER131 4.8 19.6 1.0
HB3 A:SER131 4.8 21.0 1.0

Reference:

R.Torres, R.Behera, T.Takehiko, J.Bradley, C.W.Goulding, E.C.Theil. D127E Ion Channel Exit Modification in Ferritin Nanocages Entraps Fe(II) and Impairs Its Distribution to Diiron Catalytic Centers To Be Published.
Page generated: Sun Dec 13 10:45:12 2020

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